Transcriptomic Profiling of Embryogenic and Non-Embryogenic Callus Provides New Insight into the Nature of Recalcitrance in Cannabis

Hesami, Mohsen; Pepe, Marco; de Ronne, Maxime; Yoosefzadeh-Najafabadi, Mohsen; Adamek, Kristian; Torkamaneh, Davoud; Jones, Andrew Maxwell Phineas

doi:10.3390/ijms241914625

Cited by 7 publications

(2 citation statements)

References 100 publications

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“…However, as the concentration increased, KIN demonstrated a dose-dependent response, leading to enhanced callus formation rate and fresh weight of callus. This suggests that KIN might play a PLOS ONE role in modulating cell division and proliferation processes during callogenesis [9,69,70]. Moreover, our study explored the effect of NAA and IBA, two auxins, on callus formation rate and callus fresh weight in petunia.…”

Section: Discussionmentioning

confidence: 96%

Enhancing petunia tissue culture efficiency with machine learning: A pathway to improved callogenesis

Rezaei,

Mirzaie-asl,

Abdollahi

et al. 2023

PLoS ONE

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The important feature of petunia in tissue culture is its unpredictable and genotype-dependent callogenesis, posing challenges for efficient regeneration and biotechnology applications. To address this issue, machine learning (ML) can be considered a powerful tool to analyze callogenesis data, extract key parameters, and predict optimal conditions for petunia callogenesis, facilitating more controlled and productive tissue culture processes. The study aimed to develop a predictive model for callogenesis in petunia using ML algorithms and to optimize the concentrations of phytohormones to enhance callus formation rate (CFR) and callus fresh weight (CFW). The inputs for the model were BAP, KIN, IBA, and NAA, while the outputs were CFR and CFW. Three ML algorithms, namely MLP, RBF, and GRNN, were compared, and the results revealed that GRNN (R2≥83) outperformed MLP and RBF in terms of accuracy. Furthermore, a sensitivity analysis was conducted to determine the relative importance of the four phytohormones. IBA exhibited the highest importance, followed by NAA, BAP, and KIN. Leveraging the superior performance of the GRNN model, a genetic algorithm (GA) was integrated to optimize the concentration of phytohormones for maximizing CFR and CFW. The genetic algorithm identified an optimized combination of phytohormones consisting of 1.31 mg/L BAP, 1.02 mg/L KIN, 1.44 mg/L NAA, and 1.70 mg/L IBA, resulting in 95.83% CFR. To validate the reliability of the predicted results, optimized combinations of phytohormones were tested in a laboratory experiment. The results of the validation experiment indicated no significant difference between the experimental and optimized results obtained through the GA. This study presents a novel approach combining ML, sensitivity analysis, and GA for modeling and predicting callogenesis in petunia. The findings offer valuable insights into the optimization of phytohormone concentrations, facilitating improved callus formation and potential applications in plant tissue culture and genetic engineering.

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Section: Discussionmentioning

confidence: 96%

Enhancing petunia tissue culture efficiency with machine learning: A pathway to improved callogenesis

Rezaei,

Mirzaie-asl,

Abdollahi

et al. 2023

PLoS ONE

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“…Zhang et al identified the upregulation of auxin synthesis-related genes (e.g, GH3.6 and PCO2 ) and the downregulation of cytokinin dehydrogenase ( CKX6 and CYP450 ) genes in the SE of in Paeonia ostii 'Fengdan' using transcriptome sequencing technology [ 14 ]. Hesami and colleagues used transcriptome sequencing and identified 1,850 genes downregulated and 1,873 genes upregulated in embryogenic callus compared to non-embryogenic callus of cannabis [ 15 ], including 42 different TF classes (e.g., MYB, C2H2, ERF, AP2, bHLH, bZIP, B3, WRKY and GRAS ). Hou et al used LC-MS/MS (liquid chromatography with tandem mass spectrometry) and identified 6,269 differentially expressed proteins (DEPs) in three stages (the primary embryogenic callus, the single embryo, and the cotyledon embryo) of SE in Larix olgensis , including 18 TF families were identified, including 18 TFs from the AP2, NAM and WOX families [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

Integration analysis of transcriptome and proteome profiles brings new insights of somatic embryogenesis of two eucalyptus species

Chen,

Guo,

Deng

et al. 2024

BMC Plant Biol

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Background Somatic embryogenesis (SE) is recognized as a promising technology for plant vegetative propagation. Although previous studies have identified some key regulators involved in the SE process in plant, our knowledge about the molecular changes in the SE process and key regulators associated with high embryogenic potential is still poor, especially in the important fiber and energy source tree – eucalyptus. Results In this study, we analyzed the transcriptome and proteome profiles of E. camaldulensis (with high embryogenic potential) and E. grandis x urophylla (with low embryogenic potential) in SE process: callus induction and development. A total of 12,121 differentially expressed genes (DEGs) and 3,922 differentially expressed proteins (DEPs) were identified in the SE of the two eucalyptus species. Integration analysis identified 1,353 (131 to 546) DEGs/DEPs shared by the two eucalyptus species in the SE process, including 142, 13 and 186 DEGs/DEPs commonly upregulated in the callus induction, maturation and development, respectively. Further, we found that the trihelix transcription factor ASR3 isoform X2 was commonly upregulated in the callus induction of the two eucalyptus species. The SOX30 and WRKY40 TFs were specifically upregulated in the callus induction of E. camaldulensis. Three TFs (bHLH62, bHLH35 isoform X2, RAP2-1) were specifically downregulated in the callus induction of E. grandis x urophylla. WGCNA identified 125 and 26 genes/proteins with high correlation (Pearson correlation > 0.8 or < -0.8) with ASR3 TF in the SE of E. camaldulensis and E. grandis x urophylla, respectively. The potential target gene expression patterns of ASR3 TF were then validated using qRT-PCR in the material. Conclusions This is the first time to integrate multiple omics technologies to study the SE of eucalyptus. The findings will enhance our understanding of molecular regulation mechanisms of SE in eucalyptus. The output will also benefit the eucalyptus breeding program.

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Using advanced biotechnological techniques to improve cannabis cultivars

Shujat,

Robinson,

Norouzkhani

et al. 2024

Biocatalysis and Agricultural Biotechnology

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Transcriptomic Profiling of Embryogenic and Non-Embryogenic Callus Provides New Insight into the Nature of Recalcitrance in Cannabis

Cited by 7 publications

References 100 publications

Enhancing petunia tissue culture efficiency with machine learning: A pathway to improved callogenesis

Enhancing petunia tissue culture efficiency with machine learning: A pathway to improved callogenesis

Integration analysis of transcriptome and proteome profiles brings new insights of somatic embryogenesis of two eucalyptus species

Using advanced biotechnological techniques to improve cannabis cultivars

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